Coexpression cluster:C4449

Full id: C4449_brain_temporal_occipital_cerebellum_duodenum_Neurons_parietal

Phase1 CAGE Peaks

Hg19::chr5:111092930..111092941,-	p7@C5orf13
Hg19::chr5:111093123..111093136,-	p6@C5orf13
Hg19::chr5:111093169..111093178,-	p8@C5orf13

Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

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No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

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No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

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Cell Type

Ontology term	p-value	n
non-terminally differentiated cell	2.14e-08	180

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	1.83e-25	94
nervous system	1.83e-25	94
central nervous system	7.21e-25	82
brain	1.55e-20	69
future brain	1.55e-20	69
neural tube	1.21e-17	57
neural rod	1.21e-17	57
future spinal cord	1.21e-17	57
neural keel	1.21e-17	57
regional part of brain	1.79e-17	59
ectoderm	1.06e-16	173
presumptive ectoderm	1.06e-16	173
ectoderm-derived structure	2.02e-16	169
neurectoderm	5.51e-16	90
neural plate	7.46e-16	86
presumptive neural plate	7.46e-16	86
cerebral hemisphere	9.29e-14	32
regional part of forebrain	9.65e-14	41
forebrain	9.65e-14	41
future forebrain	9.65e-14	41
cerebral cortex	1.10e-13	25
pallium	1.10e-13	25
telencephalon	1.69e-13	34
regional part of cerebral cortex	4.81e-13	22
head	4.83e-13	123
regional part of telencephalon	6.70e-13	33
gray matter	6.75e-13	34
brain grey matter	6.75e-13	34
anterior neural tube	9.10e-13	42
anterior region of body	1.01e-12	129
craniocervical region	1.01e-12	129
neocortex	2.41e-12	20
pre-chordal neural plate	1.16e-11	61
tube	1.35e-11	194
organism subdivision	1.47e-10	365
multi-cellular organism	1.61e-10	659
cell layer	3.38e-10	312
epithelium	4.74e-10	309
anatomical conduit	1.11e-07	241
anatomical cluster	1.51e-07	286
embryo	7.48e-07	612

Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

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Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115618304192946
CTBP2#1488	3	62.7170003393281	4.049570681927e-06	0.000130213396690201
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0280798067686655
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00172191331920963
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327013858589421
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0168118385983957
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00435359827956413
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157401647711456
MAFF#23764	3	56.3153564899452	5.59409009993116e-06	0.00016919813957333
MAFK#7975	3	27.1007331378299	5.02195559325033e-05	0.000858830882926922
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.0066713769741867
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00310338735909127
STAT1#6772	3	20.7065874971992	0.000112599244104667	0.00155244256832308
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00644753714635265
YY1#7528	3	4.91117074985386	0.00844145534180826	0.033073872840753
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109870971605271
ZZZ3#26009	3	239.413212435233	7.25894005043406e-08	4.38217595333689e-06

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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This analysis result is provided for C0 - C305 clusters.